bias_lineplot: Bias line plot

In dunbarlabNIH/barcodetrackR: Functions for Analyzing Cellular Barcoding Data

Description

Given a summarized experiment and a specified factor to compare bias between "split_bias_on", shows the value of that bias plotted against another specified factor "split_bias_over" where each clone is represented by a line shaded by its overall abundance in the two samples being compared.

Usage

bias_lineplot(
  your_SE,
  split_bias_on,
  bias_1,
  bias_2,
  split_bias_over,
  bias_over = NULL,
  remove_unique = FALSE,
  text_size = 16,
  keep_numeric = TRUE,
  return_table = FALSE
)

Arguments

your_SE	SummarizedExperiment of barcode data and associated metadata
split_bias_on	The column of metadata corresponding to cell types (or other factor to be compared.)
bias_1	The first cell type (or other factor) to be compared. Must be a possible value of the split_bias_on column of your metadata. Will be on the UPPER side of the line plot
bias_2	The second cell type (or other factor) to be compared. Must be a possible value of the split_bias_on column of your metadata. Will be on the LOWER side of the line plot
split_bias_over	The column of metadata to plot by. If numeric, y axis will be in increasing order. If categorical, it will follow order of metadata.
bias_over	Choice(s) from the column designated in 'split_bias_over' that will be used for plotting. Defaults to all.
remove_unique	Logical. If set to true, only clones present in both samples will be considered.
text_size	Numeric. The size of the text in the plot.
keep_numeric	Logical. Whether to keep the numeric spacing within split_bias_over or switch to discrete x scale.
return_table	Logical. If set to TRUE, rather than returnign a plot, the function will return a dataframe containing for each barcode sequence and each point of comparison: the bias value, the added proportion between the two factors at that point (cumul_sum), and the maximum cumul_sum (peak_abundance) of that barcode sequence at any point of comparison.

Value

Bias line plot for two lineages over time. Or if return_table is set to TRUE, a dataframe containing the bias values for each barcode sequence between the two samples at all points of comparison.

Examples

data(wu_subset)
bias_lineplot(
    your_SE = wu_subset, split_bias_on = "celltype",
    bias_1 = "B", bias_2 = "T", split_bias_over = "months"
)

dunbarlabNIH/barcodetrackR documentation built on April 26, 2021, 6:20 p.m.